R -e "rmarkdown::render('allTrap_familytree_histogramD.Rmd')"

Run Rmd file from command line

Need to install pandoc first
https://github.com/jgm/pandoc/releases/tag/2.1.1

$R -e "rmarkdown::render('allTrap_familytree_histogramD.Rmd')"

see 

https://github.com/rstudio/rmarkdown/issues/1100